Exception in thread "main" java.lang.NumberFormatException

[LiTing99-cutie]

Hi, i am trying to use java -jar PDV-2.1.0.jar to export some of the my spectrums, i tested psm.tsv and pep.xml for rt input and calibrated.mzML for st input like this
rt_1=../CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/psm.tsv rt_2=../CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pep.xml and st_2=../CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_calibrated.mzML

both of them came from the output of fragpipe, and my raw file format is .d, which is bruker tdf file.

I used the following commands and they both failed, can you help me to fix this? Thank you!

Exception in thread "main" java.lang.NumberFormatException: For input string: "CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.00083.00083.4"
java -jar PDV-2.1.0.jar -r $rt_1 -rt 4 -s $st_2 -st 2 -i ../spectrum_scan_number.txt -k s -o output_F2 -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
java -jar PDV-2.1.0.jar -r $rt_2 -rt 2 -s $st_2 -st 2 -i ../spectrum_scan_number.txt -k s -o output_F2 -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf

../spectrum_scan_number.txt contains only a single number.

[KaiLiCn]

Hi,

What's the FragPipe version? Can you share your FragPipe log file with me? I will test the batch model based on the same version result.

Best,
Kai

[LiTing99-cutie]

Hi,

What's the FragPipe version? Can you share your FragPipe log file with me? I will test the batch model based on the same version result.

Best, Kai

I am using the Fragpipe v22.0. Thank you for your timely reply.

Here is the log file.
log_2024-12-17_18-06-59.txt

[KaiLiCn]

Hi,

I found one bug related to the result file format changes. Unfortunately, I still need some time to fix it. You could try to export spectrum in batch using FragPipe-PDV, which is integrated into FragPipe. Here is the tutorial: https://github.com/Nesvilab/FragPipe-PDV/blob/master/FragPipe-PDV%20tutorial.pdf

Best,
Kai